---
name: "run_lefse"
section: "1"
platform: "linux"
package: "lefse"
version: "1.0.8-3"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/run_lefse"
---

# run\_lefse(1)

determine features of organisms, clades, taxonomic units, genes

## NAME

run\_lefse - determine features of organisms, clades, taxonomic units, genes

## SYNOPSIS

**run\_lefse** \[-h\] \[-o str\] \[-a float\] \[-w float\] \[-l float\] \[--nlogs int\] \[--verbose int\] \[--wilc int\] \[-r str\] \[--svm\_norm int\] \[-b int\] \[-e int\] \[-c int\] \[-f float\] \[-s {0,1,2}\] \[--min\_c int\] \[-t str\] \[-y {0,1}\] INPUT\_FILE OUTPUT\_FILE

## DESCRIPTION

LEfSe 1.0

## OPTIONS

### positional arguments:

- INPUT\_FILE

  the input file

- OUTPUT\_FILE

  the output file containing the data for the visualization module

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-o** str

  set the file for exporting the result (only concise textual form)

- **-a** float

  set the alpha value for the Anova test (default 0.05)

- **-w** float

  set the alpha value for the Wilcoxon test (default 0.05)

- **-l** float

  set the threshold on the absolute value of the logarithmic LDA score (default 2.0)

- **--nlogs** int

  max log ingluence of LDA coeff

- **--verbose** int

  verbose execution (default 0)

- **--wilc** int

  whether to perform the Wicoxon step (default 1)

- **-r** str

  select LDA or SVM for effect size (default LDA)

- **--svm\_norm** int

  whether to normalize the data in \[0,1\] for SVM feature waiting (default 1 strongly suggested)

- **-b** int

  set the number of bootstrap iteration for LDA (default 30)

- **-e** int

  set whether perform the wilcoxon test only among the subclasses with the same name (default 0)

- **-c** int

  set whether perform the wilcoxon test ing the Curtis's approach \[BETA VERSION\] (default 0)

- **-f** float

  set the subsampling fraction value for each bootstrap iteration (default 0.66666)

- **-s** {0,1,2}

  set the multiple testing correction options. 0 no correction (more strict, default), 1 correction for independent comparisons, 2 correction for independent comparison

- **--min\_c** int

  minimum number of samples per subclass for performing wilcoxon test (default 10)

- **-t** str

  set the title of the analysis (default input file without extension)

- **-y** {0,1}

  (for multiclass tasks) set whether the test is performed in a one-against-one ( 1 - more strict!) or in a one-againstall setting ( 0 - less strict) (default 0)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.